1
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Sun Y, Shao X, Zhang Y, Han L, Huang J, Xie Y, Liu J, Deng X. Maintenance of tRNA and elongation factors supports T3SS proteins translational elongations in pathogenic bacteria during nutrient starvation. Cell Biosci 2022; 12:147. [PMID: 36064743 PMCID: PMC9446538 DOI: 10.1186/s13578-022-00884-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 08/13/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Sufficient nutrition contributes to rapid translational elongation and protein synthesis in eukaryotic cells and prokaryotic bacteria. Fast synthesis and accumulation of type III secretion system (T3SS) proteins conduce to the invasion of pathogenic bacteria into the host cells. However, the translational elongation patterns of T3SS proteins in pathogenic bacteria under T3SS-inducing conditions remain unclear. Here, we report a mechanism of translational elongation of T3SS regulators, effectors and structural protein in four model pathogenic bacteria (Pseudomonas syringae, Pseudomonas aeruginosa, Xanthomonas oryzae and Ralstonia solanacearum) and a clinical isolate (Pseudomonas aeruginosa UCBPP-PA14) under nutrient-limiting conditions. We proposed a luminescence reporter system to quantitatively determine the translational elongation rates (ERs) of T3SS regulators, effectors and structural protein under different nutrient-limiting conditions and culture durations.
Results
The translational ERs of T3SS regulators, effectors and structural protein in these pathogenic bacteria were negatively regulated by the nutrient concentration and culture duration. The translational ERs in 0.5× T3SS-inducing medium were the highest of all tested media. In 1× T3SS-inducing medium, the translational ERs were highest at 0 min and then rapidly decreased. The translational ERs of T3SS regulators, effectors and structural protein were inhibited by tRNA degradation and by reduced levels of elongation factors (EFs).
Conclusions
Rapid translational ER and synthesis of T3SS protein need adequate tRNAs and EFs in nutrient-limiting conditions. Numeric presentation of T3SS translation visually indicates the invasion of bacteria and provides new insights into T3SS expression that can be applied to other pathogenic bacteria.
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2
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Yikilmaz E, Chapman SJ, Schrader JM, Uhlenbeck OC. The interface between Escherichia coli elongation factor Tu and aminoacyl-tRNA. Biochemistry 2014; 53:5710-20. [PMID: 25094027 PMCID: PMC4159200 DOI: 10.1021/bi500533x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Nineteen of the highly conserved
residues of Escherichia
coli (E. coli) Elongation factor Tu (EF-Tu)
that form the binding interface with aa-tRNA were mutated to alanine
to better understand how modifying the thermodynamic properties of
EF-Tu–tRNA interaction can affect the decoding properties of
the ribosome. Comparison of ΔΔGo values for binding EF-Tu to aa-tRNA show that the majority of the
interface residues stabilize the ternary complex and their thermodynamic
contribution can depend on the tRNA species that is used. Experiments
with a very tight binding mutation of tRNATyr indicate
that interface amino acids distant from the tRNA mutation can contribute
to the specificity. For nearly all of the mutations, the values of
ΔΔGo were identical to those
previously determined at the orthologous positions of Thermus
thermophilus (T. thermophilus) EF-Tu indicating
that the thermodynamic properties of the interface were conserved
between distantly related bacteria. Measurement of the rate of GTP
hydrolysis on programmed ribosomes revealed that nearly all of the
interface mutations were able to function in ribosomal decoding. The
only interface mutation with greatly impaired GTPase activity was
R223A which is the only one that also forms a direct contact with
the ribosome. Finally, the ability of the EF-Tu interface mutants
to destabilize the EF-Tu–aa-tRNA interaction on the ribosome
after GTP hydrolysis were evaluated by their ability to suppress the
hyperstable T1 tRNATyr variant where EF-Tu release is sufficiently
slow to limit the rate of peptide bond formation (kpep) . In general, interface mutations that destabilize
EF-Tu binding are also able to stimulate kpep of T1 tRNATyr, suggesting that the thermodynamic properties
of the EF-Tu–aa-tRNA interaction on the ribosome are quite
similar to those found in the free ternary complex.
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Affiliation(s)
- Emine Yikilmaz
- Department of Molecular Biosciences, Northwestern University , Evanston, Illinois 60208, United States
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3
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Fung AWS, Leung CCY, Fahlman RP. The determination of tRNALeu recognition nucleotides for Escherichia coli L/F transferase. RNA (NEW YORK, N.Y.) 2014; 20:1210-1222. [PMID: 24935875 PMCID: PMC4105747 DOI: 10.1261/rna.044529.114] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 04/28/2014] [Indexed: 06/03/2023]
Abstract
Escherichia coli leucyl/phenylalanyl-tRNA protein transferase catalyzes the tRNA-dependent post-translational addition of amino acids onto the N-terminus of a protein polypeptide substrate. Based on biochemical and structural studies, the current tRNA recognition model by L/F transferase involves the identity of the 3' aminoacyl adenosine and the sequence-independent docking of the D-stem of an aminoacyl-tRNA to the positively charged cluster on L/F transferase. However, this model does not explain the isoacceptor preference observed 40 yr ago. Using in vitro-transcribed tRNA and quantitative MALDI-ToF MS enzyme activity assays, we have confirmed that, indeed, there is a strong preference for the most abundant leucyl-tRNA, tRNA(Leu) (anticodon 5'-CAG-3') isoacceptor for L/F transferase activity. We further investigate the molecular mechanism for this preference using hybrid tRNA constructs. We identified two independent sequence elements in the acceptor stem of tRNA(Leu) (CAG)-a G₃:C₇₀ base pair and a set of 4 nt (C₇₂, A₄:U₆₉, C₆₈)-that are important for the optimal binding and catalysis by L/F transferase. This maps a more specific, sequence-dependent tRNA recognition model of L/F transferase than previously proposed.
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Affiliation(s)
- Angela Wai Shan Fung
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
| | | | - Richard Peter Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7 Department of Oncology, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
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4
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Abstract
Bacterial growth is crucially dependent on protein synthesis and thus on the cellular abundance of ribosomes and related proteins. Here, we show that the slow diffusion of the bulky tRNA complexes in the crowded cytoplasm imposes a physical limit on the speed of translation, which ultimately limits the rate of cell growth. To study the required allocation of ancillary translational proteins to alleviate the effect of molecular crowding, we develop a model for cell growth based on a coarse-grained partitioning of the proteome. We find that coregulation of ribosome- and tRNA-affiliated proteins is consistent with measured growth-rate dependencies and results in near-optimal allocation over a broad range of growth rates. The analysis further resolves a long-standing controversy in bacterial growth physiology concerning the growth-rate dependence of translation speed and serves as a caution against premature identification of phenomenological parameters with mechanistic processes.
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5
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Chapman SJ, Schrader JM, Uhlenbeck OC. Histidine 66 in Escherichia coli elongation factor tu selectively stabilizes aminoacyl-tRNAs. J Biol Chem 2011; 287:1229-34. [PMID: 22105070 DOI: 10.1074/jbc.m111.294850] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The universally conserved His-66 of elongation factor Tu (EF-Tu) stacks on the side chain of the esterified Phe of Phe-tRNA(Phe). The affinities of eight aminoacyl-tRNAs were differentially destabilized by the introduction of the H66A mutation into Escherichia coli EF-Tu, whereas Ala-tRNA(Ala) and Gly-tRNA(Gly) were unaffected. The H66F and H66W proteins each show a different pattern of binding of 10 different aminoacyl-tRNAs, clearly showing that this position is critical in establishing the specificity of EF-Tu for different esterified amino acids. However, the H66A mutation does not greatly affect the ability of the ternary complex to bind ribosomes, hydrolyze GTP, or form dipeptide, suggesting that this residue does not directly participate in ribosomal decoding. Selective mutation of His-66 may improve the ability of certain unnatural amino acids to be incorporated by the ribosome.
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Affiliation(s)
- Stephen J Chapman
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
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6
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Perla-Kajan J, Lin X, Cooperman BS, Goldman E, Jakubowski H, Knudsen CR, Mandecki W. Properties of Escherichia coli EF-Tu mutants designed for fluorescence resonance energy transfer from tRNA molecules. Protein Eng Des Sel 2010; 23:129-36. [PMID: 20083494 DOI: 10.1093/protein/gzp079] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Here we describe the design, preparation and characterization of 10 EF-Tu mutants of potential utility for the study of Escherichia coli elongation factor Tu (EF-Tu) interaction with tRNA by a fluorescence resonance energy transfer assay. Each mutant contains a single cysteine residue at positions in EF-Tu that are proximal to tRNA sites within the aminoacyl-tRNA.EF-Tu.GTP ternary complex that have previously been labeled with fluorophores. These positions fall in the 323-326 and 344-348 regions of EF-Tu, and at the C terminus. The EF-Tus were isolated as N-terminal fusions to glutathione S-transferase (GST), which was cleaved to yield intact EF-Tus. The mutant EF-Tus were tested for binding to GDP, binding to tRNA in gel retardation and protection assays, and activity in poly-U translation in vitro. The results indicate that at least three EF-Tu mutants, K324C, G325C and E348C, are suitable for further studies. Remarkably, GST fusions that were not cleaved were also active in the various assays, despite the N-terminal fusion.
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Affiliation(s)
- Joanna Perla-Kajan
- Department of Microbiology and Molecular Genetics, UMDNJ-New Jersey Medical School, Newark, 07101, USA
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7
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Dahl LD, Wieden HJ, Rodnina MV, Knudsen CR. The importance of P-loop and domain movements in EF-Tu for guanine nucleotide exchange. J Biol Chem 2006; 281:21139-21146. [PMID: 16717093 DOI: 10.1074/jbc.m602068200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Elongation factor Ts (EF-Ts) is the guanine nucleotide exchange factor for elongation factor Tu (EF-Tu). An important feature of the nucleotide exchange is the structural rearrangement of EF-Tu in the EF-Tu.EF-Ts complex caused by insertion of Phe-81 of EF-Ts between His-84 and His-118 of EF-Tu. In this study, the contribution of His-118 to nucleotide release was studied by pre-steady state kinetic analysis of nucleotide exchange in EF-Tu mutants in which His-118 was replaced by Ala or Glu. Intrinsic as well as EF-Ts-catalyzed release of GDP/GTP was affected by the mutations, resulting in an approximately 10-fold faster spontaneous nucleotide release and a 10-50-fold slower EF-Ts-catalyzed nucleotide release. The effects are attributed to the interference of the mutations with the EF-Ts-induced movements of the P-loop of EF-Tu and changes at the domain 1/3 interface, leading to the release of the beta-phosphate group of GTP/GDP. The K(d) for GTP is increased by more than 40 times when His-118 is replaced with Glu, which may explain the inhibition by His-118 mutations of aminoacyl-tRNA binding to EF-Tu. The mutations had no effect on EF-Tu-dependent delivery of aminoacyl-tRNA to the ribosome.
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Affiliation(s)
- Louise D Dahl
- Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Århus C, Denmark
| | - Hans-Joachim Wieden
- Institute of Physical Biochemistry, University of Witten/Herdecke, Stockumer Strasse 10, D-58448 Witten, Germany
| | - Marina V Rodnina
- Institute of Physical Biochemistry, University of Witten/Herdecke, Stockumer Strasse 10, D-58448 Witten, Germany
| | - Charlotte R Knudsen
- Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Århus C, Denmark.
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8
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Vorstenbosch EL, Potapov AP, de Graaf JM, Kraal B. The effect of mutations in EF-Tu on its affinity for tRNA as measured by two novel and independent methods of general applicability. JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS 2000; 42:1-14. [PMID: 10647810 DOI: 10.1016/s0165-022x(99)00032-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Elongation factor Tu is essential for binding and a correct delivery of aminoacyl-tRNA during protein biosynthesis. For a good characterization of its interaction with tRNA in terms of structure-function relationship, determinations of kinetic equilibrium parameters are of great value. We describe two novel methods for that purpose. One method is based on EF-Tu protection of the tRNA 3' acceptor end against RNase A cleavage and yields the Kd value together with the corresponding dissociation and association rate constants from one single set of experiments. The other is a rapid method for screening relative affinities of mutant EF-Tus for tRNA. It is based on competition between EF-Tu species with and without a (His)6 extension for the same aminoacyl-tRNA and yields a relative Kd value. The method can be of general importance for the measuring of ligand affinities of all sorts of His-tagged proteins. Both methods are illustrated by their application in the analysis of mutant EF-Tus with changed interactions with tRNA and antibiotics. Raising the assay temperature from 4 to 37 degrees C causes a 30-fold increase of Kd for EF-Tu x GTP x Phe-tRNA complexes. The mutation K237E leads to rapid inactivation at the latter temperature. A parallel is found between the order of increasing Kd values for EF-Tus with mutation G316D, A375T and Q124K, respectively, and their order of increasing resistance to kirromycin.
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Affiliation(s)
- E L Vorstenbosch
- Department of Biochemistry, Leiden Institute of Chemistry, Leiden University, The Netherlands
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9
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Abstract
In our previous work (Mansilla et al. (1997) Protein Eng. 10, 927-934) we showed that Arg7 of Escherichia coli elongation factor Tu (EF1A) plays an essential role in aminoacyl-tRNA (aa-tRNA) binding. Substitution of Arg7 by Ala or Glu lost this activity. We proposed that Arg7 forms a salt bridge with the charged conserved amino acid Glu272 (Asp284 in Thermus aquaticus) thereby binding the N-terminal region of the protein to domain 2 and thus completing the conformational rearrangement needed for binding aa-tRNA. In this work we have mutated Glu272 to arginine, either alone (Glu272Arg), or in combination with one of the above mentioned mutations (Arg7Glu/Glu272Arg) in order to test this hypothesis. Our results show that, in confirmation of our thesis based on structural knowledge, the substitution of Glu272 (Asp284) decreases the ability of EF1A:GTP to bind aa-tRNA.
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Affiliation(s)
- F Mansilla
- Institute of Molecular and Structural Biology, Aarhus University, Aarhus C, Denmark
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10
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Laurberg M, Mansilla F, Clark BF, Knudsen CR. Investigation of functional aspects of the N-terminal region of elongation factor Tu from Escherichia coli using a protein engineering approach. J Biol Chem 1998; 273:4387-91. [PMID: 9468489 DOI: 10.1074/jbc.273.8.4387] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The function of the N-terminal region of elongation factor Tu is still unexplained. Until recently, it has not been visible in electron density maps from x-ray crystallography studies, but the presence of several well conserved basic residues suggest that this part of the molecule is of structural importance for the factor to function properly. In this study, two lysines at positions 4 and 9 were mutated separately to alanine or glutamate. The resulting four point mutants were expressed and purified using the pGEX system. The untagged products were characterized with regard to guanine-nucleotide interaction, intrinsic GTPase activity, and binding of aminoacyl-tRNA (aa-tRNA). The results show that Lys9 is especially strongly involved in the association with guanine nucleotides and the binding of aa-tRNA. Also Lys4 plays a role in the association of GDP and GTP and is also of some importance in aa-tRNA binding. Our results are discussed in structural terms with the conclusion that a complex network of interactions across the interface between domains 1 and 2 with Lys9 being a key residue seems to be important for the fine tuning of the dimensions of the cleft accommodating the acceptor end of aa-tRNA as well as delineating the structure of the effector region.
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Affiliation(s)
- M Laurberg
- Lund University, Molecular Biophysics, Box 124, S-22100 Lund, Sweden
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11
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Jonák J, Anborgh PH, Parmeggiani A. Interaction of EF-Tu with EF-Ts: substitution of His-118 in EF-Tu destabilizes the EF-Tu x EF-Ts complex but does not prevent EF-Ts from stimulating the release of EF-Tu-bound GDP. FEBS Lett 1998; 422:189-92. [PMID: 9490003 DOI: 10.1016/s0014-5793(98)00007-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Elongation factor Tu from Escherichia coli with His-118 substituted by glycine (EF-TuH118G) was found to be defective in complex formation with EF-Ts. EF-Ts in excess failed to dissociate kirromycin from the EF-TuH118G x kirromycin complex and to form a stable complex with EF-TuH118G on column chromatography. However, the stimulatory effect of EF-Ts on GDP dissociation from EF-TuH118G x GDP and on poly(U)-directed poly(Phe) synthesis catalyzed by EF-TuH118G was only partially influenced. These results indicate that His-118, while very important for the formation of a stable EF-Tu-EF-Ts complex, is not essential for the transmission of the EF-Ts-dependent signal accelerating the release of the EF-Tu-bound GDP.
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Affiliation(s)
- J Jonák
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague.
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12
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Ling M, Merante F, Chen HS, Duff C, Duncan AM, Robinson BH. The human mitochondrial elongation factor tu (EF-Tu) gene: cDNA sequence, genomic localization, genomic structure, and identification of a pseudogene. Gene 1997; 197:325-36. [PMID: 9332382 DOI: 10.1016/s0378-1119(97)00279-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The human mitochondrial elongation factor Tu (EF-Tu) is nuclear-encoded and functions in the translational apparatus of mitochondria. The complete human EF-Tu cDNA sequence of 1677 base pairs (bp) with a 101 bp 5'-untranslated region, a 1368 bp coding region, and a 207 bp 3'-untranslated region, has been determined and updated. The predicted protein from this cDNA sequence is approximately 49.8 kDa in size and is composed of 455 amino acids (aa) with a putative N-terminal mitochondrial leader sequence of approximately 50 aa residues. The predicted amino acid sequence shows high similarity to other EF-Tu protein sequences from ox, yeast, and bacteria, and also shows limited similarity to human cystolic elongation factor 1 alpha. The complete size of this cDNA (1677 bp) obtained by cloning and sequencing was confirmed by Northern blot analysis, which showed a single transcript (mRNA) of approximately 1.7 kb in human liver. The genomic structure of this EF-Tu gene has been determined for the first time. This gene contains nine introns with a predicted size of approximately 3.6 kilobases (kb) and has been mapped to chromosome 16p11.2. In addition, an intronless pseudogene of approximately 1.7 kb with 92.6% nucleotide sequence similarity to the EF-Tu gene has also been identified and mapped to chromosome 17q11.2.
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MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence
- Cell Line
- Chromosome Mapping
- Chromosomes, Human, Pair 16/genetics
- Chromosomes, Human, Pair 17/genetics
- Cloning, Molecular
- Cricetinae
- DNA, Complementary/genetics
- Genes/genetics
- Humans
- Hybrid Cells
- Introns/genetics
- Liver/chemistry
- Molecular Sequence Data
- Peptide Elongation Factor Tu/genetics
- Pseudogenes/genetics
- RNA, Messenger/analysis
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- M Ling
- Department of Genetics, Hospital for Sick Children, Toronto, Ontario, Canada
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13
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Wiborg O, Andersen C, Knudsen CR, Clark BF, Nyborg J. Mapping Escherichia coli elongation factor Tu residues involved in binding of aminoacyl-tRNA. J Biol Chem 1996; 271:20406-11. [PMID: 8702777 DOI: 10.1074/jbc.271.34.20406] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Two residues of Escherichia coli elongation factor Tu involved in binding of aminoacyl-tRNA were identified and subjected to mutational analysis. Lys-89 and Asn-90 were each replaced by either Ala or Glu. The four single mutants were denoted K89A, K89E, N90A, and N90E, respectively. The mutants were characterized with respect to thermal and chemical stability, GTPase activity, tRNA affinity, and activity in an in vitro translation assay. Most conspicuously tRNA affinities were reduced for all mutants. The results verify our structural analysis of elongation factor Tu in complex with aminoacyl-tRNA, which suggested an important role of Lys-89 and Asn-90 in tRNA binding. Furthermore, our results indicate helix B to be an important target site for nucleotide exchange factor EF-Ts. Also the mutants His-66 to Ala and His-118 to either Ala or Glu were characterized in an in vitro translation assay. Their functional roles are discussed in relation to the structure of elongation factor Tu in complex with aminoacyl-tRNA.
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Affiliation(s)
- O Wiborg
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
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14
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Abstract
Five single amino acid substitution variants of EF-Tu from Salmonella typhimurium were tested for their ability to promote poly(U)-translation in vitro. The substitutions are Leu120 Gln, Gln124 Arg and Tyr160 (Asp or Asn or Cys). They were selected by their kirromycin resistant phenotypes and all substitutions are in domain I at the interface between domains I and III of the EF-Tu.GTP configuration. The different EF-Tu variants exhibit a spectrum of phenotypes. First, k cat/K(M) for the interaction between ternary complex and the programmed ribosome is apparently reduced by the substitutions Leu120 Gln, Gln124 Arg and Tyr160 Cys. Second, this reduction is caused by a defect in the interaction between these EF-Tu variants and aminoacyl-tRNA during translation. Third, in four cases out of five the affinity of the complex between EF-Tu.GTP and aminoacyl-tRNA is significantly decreased. The most drastic reduction is observed for the Gln124 Arg change, where the association constant is 30-fold lower than in the wild-type case. Fourth, missense errors are increased as well as decreased by the different amino acid substitutions. Finally, the dissociation rate constant (kd) for the release of GDP from EF-Tu is increased 6-fold by the Tyr160 Cys substitution, but remains unchanged in the four other cases. These results show that the formation of ternary complex is sensitive to many different alterations in the domain I-III interface of EF-Tu.
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Affiliation(s)
- F Abdulkarim
- Department of Molecular Biology, The Biomedical Center, Uppsala University, Sweden
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15
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Nissen P, Kjeldgaard M, Thirup S, Polekhina G, Reshetnikova L, Clark BF, Nyborg J. Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog. Science 1995; 270:1464-72. [PMID: 7491491 DOI: 10.1126/science.270.5241.1464] [Citation(s) in RCA: 652] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The structure of the ternary complex consisting of yeast phenylalanyl-transfer RNA (Phe-tRNAPhe), Thermus aquaticus elongation factor Tu (EF-Tu), and the guanosine triphosphate (GTP) analog GDPNP was determined by x-ray crystallography at 2.7 angstrom resolution. The ternary complex participates in placing the amino acids in their correct order when messenger RNA is translated into a protein sequence on the ribosome. The EF-Tu-GDPNP component binds to one side of the acceptor helix of Phe-tRNAPhe involving all three domains of EF-Tu. Binding sites for the phenylalanylated CCA end and the phosphorylated 5' end are located at domain interfaces, whereas the T stem interacts with the surface of the beta-barrel domain 3. The binding involves many conserved residues in EF-Tu. The overall shape of the ternary complex is similar to that of the translocation factor, EF-G-GDP, and this suggests a novel mechanism involving "molecular mimicry" in the translational apparatus.
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Affiliation(s)
- P Nissen
- Department of Biostructural Chemistry, Institute of Chemistry, Aarhus University, Denmark
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16
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Abstract
The past year has witnessed a tremendous increase in our understanding of the structures and interactions of the GTPases. The highlights include crystal structures of G alpha subunits, as well as the first complex between a GTPase (Rap1A) and an effector molecule (c-Raf1 Ras-binding domain). In the field of elongation factors (EFs), three very important structures have been determined: EF-G, the ternary complex of EF-Tu.GTP with aminoacyl-tRNA, and the EF-Tu.EF-Ts complex.
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Affiliation(s)
- R Hilgenfeld
- Institute of Molecular Biotechnology, Jena, Germany
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17
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Kjaersgård IV, Knudsen CR, Wiborg O. Mutation of the conserved Gly83 and Gly94 in Escherichia coli elongation factor Tu. Indication of structural pivots. EUROPEAN JOURNAL OF BIOCHEMISTRY 1995; 228:184-90. [PMID: 7883002 DOI: 10.1111/j.1432-1033.1995.tb20248.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Elongation factor Tu from Escherichia coli cycles between an active conformation where GTP is bound, and an inactive conformation where GDP is bound. Between the two conformations, elongation factor Tu undergoes major structural changes. The aim of this work has been to reveal the role of two very well conserved glycine residues, Gly83 and Gly94, in the switch mechanism. Gly83 has been mutated alone or in combination with Gly94, both glycine residues being mutated to alanine. Enzymic characterisation of the two mutants have shown that they have an altered nucleotide affinity, a decrease in aminoacyl-tRNA affinity, an increase in intrinsic GTP hydrolysis, different behaviours in effector stimulation of the intrinsic GTPase activity, and that they are completely unable to sustain poly(Phe) synthesis in an in-vitro poly(U)-directed system. Our results indicates that particularly Gly83 is an important pivot point in elongation factor-Tu.
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18
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Knudsen CR, Kjaersgard IVH, Wiborg O, Clark BFC. Mutation of the Conserved Gly94 and Glyl26 in Elongation Factor Tu from Escherichia Coli. Elucidation of their Structural and Functional Roles. ACTA ACUST UNITED AC 1995. [DOI: 10.1111/j.1432-1033.1995.tb20247.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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